fix: resolve state mutation by cloning graph before json conversion in save_graph (#796)

[suhaniiz]

📋 PR Checklist

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🔗 Related Issue

Closes #796

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📝 What does this PR do?

Resolves a silent state mutation bug where processing sequential document chunks in memory caused an unhandled AttributeError.

The build_graph function was calling _convert_sets_for_json(graph) right before returning, which mutated the underlying graph's node/edge properties (pages and chunks) from mutable Python set structures into sorted list structures. Consequently, subsequent in-memory operations attempting to call .add() on these properties failed.

This PR removes the mutation call from build_graph and safely decouples serialization by calling _convert_sets_for_json() on a shallow clone (graph.copy()) inside save_graph right before writing to disk.

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🗂️ Type of Change

• 🐛 Bug fix
• ✨ New feature
• 🔧 Refactor / code cleanup
• 📝 Documentation update
• 🎨 UI / styling change
• ⚙️ CI / tooling / config change
• 🧪 Tests

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🧪 How was this tested?

• Tested the affected API endpoints manually
• Verified in-memory graph persistence structure remains intact across multi-batch processing cycles.

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📸 Screenshots (if UI change)

N/A (Backend logic fix)

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⚠️ Anything to flag for reviewers?

The fix uses a lightweight graph.copy() shallow copy from NetworkX inside save_graph. This ensures we don't manipulate the core operational graph being actively processed or maintained in memory while fully isolating the structural type adjustments needed strictly for JSON compliance.

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✅ Self-Review Checklist

• My branch is based on dev, not main
• I have not added any secrets / API keys
• I have not modified main branch or any HuggingFace deployment config
• My code follows the existing style (no unnecessary formatting changes)
• I have updated relevant docs / comments if needed

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[suhaniiz]

@param20h , kindly review this, it is under gssoc!